Louis BECQUEY / biorseo

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Louis BECQUEY
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b220f7cc 1 parent acd90ac3

Update INSTALL.md for release ZIP

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1 Option 1 : Installation using docker image (Windows, Mac, Linux) 1 Option 1 : Installation using docker image (Windows, Mac, Linux)
2 ================================== 2 ==================================
3 -* Clone this git repository : `git clone https://github.com/persalteas/biorseo.git` 3 +* Clone this git repository : `git clone https://github.com/persalteas/biorseo.git` , or download the .zip archive from a BiORSEO release and extract it.
4 -* Move into the cloned repository ( `cd biorseo` ) 4 +* Move into the repository ( `cd biorseo` )
5 5
6 ### Install Docker: 6 ### Install Docker:
7 * See the officiel instructions depending on your OS here : https://docs.docker.com/install/ 7 * See the officiel instructions depending on your OS here : https://docs.docker.com/install/
...@@ -53,7 +53,7 @@ $ docker run ...@@ -53,7 +53,7 @@ $ docker run
53 persalteas/biorseo 53 persalteas/biorseo
54 yourexamplejobcommandhere 54 yourexamplejobcommandhere
55 ``` 55 ```
56 -You can replace \`pwd\` by the full path of the biorseo/ root folder. Here we launch the biorseo image with 4 volumes : A first to give BiORSEO access to the module files, a second to give it access to your input file(s), a third for your trained BayesPairing, and a last for it to output the result files of your job. An example job command can be ` ./biorseo.py -i /biorseo/data/fasta/applications.fa --rna3dmotifs --patternmatch --func B`, so the full run command would be 56 +You can replace \`pwd\` by the full path of the biorseo/ root folder. Here we launch the biorseo image with 4 volumes : A first to give BiORSEO access to the module files, a second to give it access to your input file(s), a third for your trained BayesPairing, and a last for it to output the result files of your job. Considering you place your input file 'MyFastaFile.fa' into the `data/fasta` folder, an example job command can be ` ./biorseo.py -i /biorseo/data/fasta/myFastaFile.fa --rna3dmotifs --patternmatch --func B`, so the full run command would be
57 ``` 57 ```
58 $ docker run -v `pwd`/data/modules:/modules -v `pwd`/data/fasta:/biorseo/data/fasta -v `pwd`/BayesPairing/bayespairing:/byp -v `pwd`/results:/biorseo/results persalteas/biorseo ./biorseo.py -i /biorseo/data/fasta/applications.fa --rna3dmotifs --patternmatch --func B 58 $ docker run -v `pwd`/data/modules:/modules -v `pwd`/data/fasta:/biorseo/data/fasta -v `pwd`/BayesPairing/bayespairing:/byp -v `pwd`/results:/biorseo/results persalteas/biorseo ./biorseo.py -i /biorseo/data/fasta/applications.fa --rna3dmotifs --patternmatch --func B
59 ``` 59 ```
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